getDEE2
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see getDEE2.
Programmatic access to the DEE2 RNA expression dataset
Bioconductor version: 3.14
Digital Expression Explorer 2 (or DEE2 for short) is a repository of processed RNA-seq data in the form of counts. It was designed so that researchers could undertake re-analysis and meta-analysis of published RNA-seq studies quickly and easily. As of April 2020, over 1 million SRA datasets have been processed. This package provides an R interface to access these expression data. More information about the DEE2 project can be found at the project homepage (http://dee2.io) and main publication (https://doi.org/10.1093/gigascience/giz022).
Author: Mark Ziemann [aut, cre], Antony Kaspi [aut]
Maintainer: Mark Ziemann <mark.ziemann at gmail.com>
citation("getDEE2")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("getDEE2")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("getDEE2")| getDEE2 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Sequencing, Software, Transcriptomics |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.0) |
| Imports | stats, utils, SummarizedExperiment, htm2txt |
| System Requirements | |
| URL | https://github.com/markziemann/getDEE2 |
See More
| Suggests | knitr, testthat, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | getDEE2_1.4.0.tar.gz |
| Windows Binary | getDEE2_1.4.0.zip |
| macOS 10.13 (High Sierra) | getDEE2_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/getDEE2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/getDEE2 |
| Bioc Package Browser | https://code.bioconductor.org/browse/getDEE2/ |
| Package Short Url | https://bioconductor.org/packages/getDEE2/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |